Genomic DNA amplifications, which lead to the increased expression of oncogenes, frequently contribute to the development of cancer. Characterizing these DNA copy number changes is important for advancing our understanding of cancer, as well as for its diagnosis and treatment. The objectives of this study are to characterize recurrent gene amplifications in breast cancer, to understand their role in tumor development and progression, and to investigate their utility as prognostic markers and therapeutic targets. The achievement of these goals relies on three recent technical developments: array-based comparative genomic hybridization (array CGH), tissue microarrays, and RNA interference (RNAi). In array CGH, tumor and normal genomic DNA are differentially labeled and co-hybridized to a microarray containing thousands of different genes. Fluorescence ratios at each element on the array provide a high resolution, "gene-by-gene" map of DNA copy number alteration across the cancer genome. Tissue microarrays consist of hundreds of different tissue biopsies from individual tumors sectioned onto a single microscope slide. Fluorescence in situ hybridization (FISH) on tissue microarrays permits the highly parallel detection of a single gene's amplification, and its correlation with clinical outcome data, for each of the specimens on the array. Finally, RNAi is the sequence-specific, post-transcriptional gone silencing initiated by double-stranded RNA that is homologous to the gene targeted. RNAi methods will permit the identification of oncogene(s) within recurrent regions of amplification, the investigation of their functional role in tumorigenesis, and an evaluation of their potential utility as targets for cancer therapy. The specific scientific aims of this proposal are: (1) to identify and map at high resolution recurrent gene amplifications in breast cancer by array CGH; (2) to evaluate gene amplifications as prognostic markers using FISH on tissue microarrays; and (3) to determine the functional role of, and therapeutic potential of targeting, identified gene amplifications in breast cancer using RNAi techniques.